title: NhaC-0M

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

institute: Meijo University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: Escherichia coli K12- W3110 (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000110)
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample

organism: Escherichia coli

source_name: NhaC Na+/H+ antiporter (H2569) -expressed TO114 strain

growth_protocol: E. coli cells were cultured at 37ºC in LBK media with 50 μg/ml of ampicillin and 25 μg/ml of kanamycin.

extract_protocol:
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
RNA samples were utilized to construct the libraries, which were sequenced.

value: control

tag: time

value: 4 h


title: SK-N-BE(2) TCF4

status: Public on May 06 2024

type: SRA

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

country: China

institute: Children’s Hospital of Soochow University

description: CUT&Tag DNA

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig files and peak text files
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Neuroblastoma cells

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

tag: cell line

tag: cell type

value: Neuroblastoma cells

tag: antibody

value: TCF4(ab217668, Abcam)


title: Tcrb_KO_MouseNo1

city: Shanghai

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Raw fastq files were first filtered by fastp (v0.22.0) to trim and remove sequencing adapters as well as low quality bases and reads.
Trimmed fastq files were then aligned to mm10 (UCSC) with bowtie2(v2.5.2) under default parameters.Reads that cannot aligned to mouse genome were extracted by samtools (v1.18)
Clean fastq files were analyzed by Kraken2 (v2.0.7-beta) software using Standard PlusPF (release 1/12/2024) database downloaded from index zone (https://benlangmead.github.io/aws-indexes/k2).
Assembly: mm10
Assembly: Kraken 2 / Bracken Refseq index
Supplementary files format and content: Table separated files containing taxonomy counts of each sample.
Supplementary files format and content: Table separated files containing KEGG orthology gene counts of each sample.
Library strategy: metagenome sequencing

organism: feces metagenome

source_name: Fecal

growth_protocol: TCRb-/- mice were freshly ordered from the Jackson laboratory

extract_protocol:
Feces were collected and DNA was extracted by QIAGEN Power Fecal Pro DNA Kit following manufacturer's instruction.
mWGS DNA library was constructed using TruSeq DNA Library Prep Kit under manufacturer's instruction for metagenomic whole-genome shotgun sequencing (mWGS)

tag: genotype

value: Tcrb-/-

tag: host

value: mouse

tag: host tissue

value: feces


title: Tcrb_KO_MouseNo5


title: NhaC-04M

country: Japan

library_source: transcriptomic

molecule: total RNA

tag: strain

value: NhaC Na+/H+ antiporter (H2569) -expressed TO114 strain

tag: treatment

value: 0.4 M NaCl stress

value: 6 h


title: S106_XBP1S_RU+_gut_rep3

city: LONDON

first: MengJia

last: Li

state: Please Select

address: flat38 midhopse house, midhope street

country: United Kingdom

institute: University College London

data_processing:
Quality control with fastqc
Alignment with hisat2
Read counts with featureCounts
Differentially expression analysis with deseq2
Salmon to confirm Xbp1U samples
Assembly: Drosophila Melanogaster dm6 (r6.47)
Supplementary files format and content: Differentially expression results for each genotype/tissues

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Gut

extract_protocol:
Trizol_cholofrom
pair-end

treatment_protocol: treat with RU486 +/- for 7 days

tag: tissue

value: Gut

value: RU+


title: S106_XBP1S_RU+_gut_rep2


title: 72hr Female Negative

city: Towada

first: Asako

last: Haraguchi

state: Aomori

department: School of Veterinary Medicine

institute: Kitasato University

data_processing:
FastQC v0.11.7 was used for performing quality check on the raw sequences before analysis to make sure data integrity.
Trimmomatic 0.38 was used for trimming to remove low quality reads, adaptor sequence, contaminant DNA, or PCR duolicates.
Trimmed reads were mapped to reference genome with HISAT2. Transcript was assembled by StringTie with aligned reads.
Expression profiles were represented as read count and FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value as a normalized value.
Assembly: AsteI2
Supplementary files format and content: The data file is text file and includes expressioin profiles of each samples.

organism: Anopheles stephensi

source_name: Whole body

extract_protocol:
Three mosquitoes were collected as one sample and stored at -80 °C. Total RNA was extracted using Nucleo Spin RNA Blood (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol, delivered to Macrogen Japan Corp. (Tokyo, Japan) for library construction using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).
Total RNA was sequenced using the NovaSeq 6000 system (Illumina).

value: Whole body

tag: gender

value: Female

value: Medium injection

tag: timepoint


title: 72hr Female Injection

value: Ookinete injection


title: SK-N-BE(2) MEIS2 rep2

description: CUT&Tag DNA

value: MEIS2(sc-515470, Santa Cruz)


title: S106_XBP1S_RU+_gut_rep1


title: Csk(f/f) #2

city: Suita-shi

first: Takeshi

last: Inoue

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

description: Csk RNA-seq.txt

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Mus musculus

source_name: spleen

growth_protocol: Csk(+/+) ERT2cre(KI/+) B1-8hi(KI/+) CD45.1/2 or Csk(fl/fl) ERT2cre(KI/+) B1-8hi(KI/+) CD45.1/2 naïve B cells were transferred into C57BL/6J mice. Mice were immunized with NP-CGG/Alum i.p on day 0, treated with Tamoxifen to induce KO on day 8 and 9, and NP+ donor GC light zone B cells were isolated by FACS sorting on day 11.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
DNA library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) from total RNA purified from ∼10^4 sorted cells.

value: spleen

value: GC light zone B cell

tag: strain background

value: Csk(f/f)

value: tamoxifen


title: SK-N-BE(2) MEIS2 rep1

description: CUT&Tag DNA

value: Neuroblastoma cells


title: 72hr Male Injection

value: Male


title: Csk(f/f) #1

description: Csk RNA-seq.txt


title: 24hr Male Negative

data_processing:
FastQC v0.11.7 was used for performing quality check on the raw sequences before analysis to make sure data integrity.
Trimmomatic 0.38 was used for trimming to remove low quality reads, adaptor sequence, contaminant DNA, or PCR duolicates.
Trimmed reads were mapped to reference genome with HISAT2. Transcript was assembled by StringTie with aligned reads.
Expression profiles were represented as read count and FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value as a normalized value.
Genome_build: AsteI2
Supplementary_files_format_and_content: The data file is text file and includes expressioin profiles of each samples.


title: SK-N-BE(2) IgG

description: CUT&Tag DNA

value: IgG(ab172730, Abcam)


title: S106_XBP1S_RU+_fb_rep4

source_name: Fat body

value: Fat body


title: Csk(+/+) #3

description: Csk RNA-seq.txt


title: 24hr Male Injection


title: S106_XBP1S_RU+_fb_rep3


title: SK-N-BE(2) HAND2 rep2

description: CUT&Tag DNA

value: HAND2(ab200040, Abcam)


title: SK-N-BE(2) HAND2 rep1

description: CUT&Tag DNA


title: Csk(+/+) #2

description: Csk RNA-seq.txt


title: S106_XBP1S_RU+_fb_rep2


title: 24hr Female Negative


title: SC340

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

country: USA

institute: University of Pittsburgh

data_processing:
10X Genomics' Cell Ranger 3.1.0 mkfastq function (a wrapper for bcl2fastq) performed basecalling to generate FASTQ files
10X Genomics' Cell Ranger 3.1.0 count function mapped the produced FASTQ files to 10X Genomics' publicly available build of GRCh38 to produce the .h5 file which combines a matrix file of UMI counts per cell (from gene expression, GEX) and a matrix file of hashtag counts per cell from feature barcoding hashtag library (HTOFB)
The output file SC340raw_feature_bc_matrix.h5 was used for further downstream analysis in R 3.6.1 using the packages Seurat 3.1.1 and SCTransform, both the gene expression and hashtag count matrix can were loaded from this processed data file
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data file .h5 contains two matrices: the first is the gene and cell barcode gene expression matrix; the second matrix contains the antibody-associated hashtag counts per cell

source_name: Whole Lung Tissue

extract_protocol:
Whole lung tissue was mechanically and enzymatically dissociated and filtered to create a single cell suspension.  Each patient sample was then cryopreserved as a single cell suspension.  Once selected, ten individual lung suspensions were thawed, incubated with a unique TotalSeq-C hashtag antibody and viability was assessed.  From each individual cell suspension, 3500 TotalSeq-C antibody hashtag-labeled cells were combined into one 10X Genomics 5Prime Immune Profiling reaction.
The gene expression (GEX) and cell hashing/feature barcode (HTOFB) libraries were constructed according to the manufacturer's protocol, specifically the Chromium Single Cell V(D)J Reagent Kits User Guide (v1 Chemistry) with Feature Barcoding technology for Cell Surface Protein

value: Lung

tag: input

value: Whole Lung Tissue Single Cell Suspension


title: Control-0M

source_name: TO114 strain

value: TO114 strain

value: control

value: 4 h


title: 24hr Female Injection

value: Female


title: Csk(+/+) #1

description: Csk RNA-seq.txt


title: S106_XBP1S_RU+_fb_rep1

value: RU+


title: 05 genetic hsp90b1-knockout Treg cells, spleen

status: Public on May 05 2024

city: Columbus

first: Yuzhou

last: Chang

state: OH

address: 5769 Privilege drive, Hilliard

institute: ohio state univeristy

data_processing:
Raw data in FASTQ format were processed through fastp to remove reads containing adapter sequences and poly-N sequences. Additionally, reads with low quality were filtered out to obtain clean data (clean reads).
Original image data files from the high-throughput sequencing platform (e.g., Illumina) were transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Assembly: mm10
Supplementary files format and content: FPKMs per sample

source_name: Spleen

extract_protocol:
RNA extraction was performed using the RNeasy Micro Kit (Qiagen) following the manufacturer's standard protocol
Libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample.
The library strategy utilized for RNA sequencing was strand-specific paired-end sequencing.

value: Spleen

value: Treg


title: 03 genetic hsp90b1-knockout Treg cells, spleen


title: 01 genetic hsp90b1-knockout Treg cells, spleen


title: 04 WT Treg cells, spleen

value: WT


title: 04 genetic hsp90b1-knockout Treg cells, spleen


title: 03 WT Treg cells, spleen


title: 02 genetic hsp90b1-knockout Treg cells, spleen


title: 01 WT Treg cells, spleen


title: Pt011_Product

city: Boston

first: Jim

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Paired GEX and VDJ libraries were aligned using the ‘Cellranger multi’ pipeline (v7.0.0) with 32 CPU’s and 128 GB of RAM, with VDJ libraries listed as “vdj-t” to indicate T cell libraries. Samples were aggregated with the ‘Cellranger aggr’ pipeline (v7.0.0) with arguments ‘--normalize=none --nosecondary’. Our reference transcriptome was created with the Cellranger makeref command, and used Homo_sapiens.GRCh38 as the reference genome and Ensembl v107 as the reference for humans.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: h5 matrix of single-cell RNA-Seq
Supplementary files format and content: Csv file of clonotype information for single-cell TCR-Seq

source_name: CAR T Product

extract_protocol:
Peripheral blood samples from pediatric patients with B-ALL receiving Trisangeleucel were collected under the Boston Children’s Hospital and Dana Farber Cancer Institute approved clinical protocol, ‘PREDICT’ (NCT03369353). Patient blood was obtained and PBMCs were isolated by Ficoll-PaquePLUS (GE Healthcare Bio-Sciences) gradient centrifugation. PBMCs were cryopreserved and stored for further use. CD19 CAR-T cells from patient samples were stained with an anti-CD19 CAR antibody (ACRO Biosystem, Cat#: CD9-HF251-25ug). CD3 flow cytometric antibodies were not utilized, to avoid in vitro stimulation, which can result in alteration of the transcriptional profile. Live CARpos and CARneg, CD4/CD8pos and CD20/CD14neg cells were flow cytometrically sorted and immediately processed for single cell sequencing.
All products used in the preparation of these samples are available from 10x Genomics. Samples in this publication were prepared using the Next GEM 5’ v2 Gel Beads with the i7 Multiplex Plate (Single Index) or the Next GEM Single Cell 5’ v2 Sample Index Plate TT (Dual Index). GEMs were generated using v2 Gel Beads and the v1 Target Enrichment kit utilizing the off-the-shelf human/mouse T Cell Mix 1 and 2 premixed primers for the patient samples.
scRNA-Seq and scTCR-Seq

tag: alt sample_name

tag: patient

value: CAR T Product


title: Pt011_CARNeg

source_name: Blood

value: Blood

value: CARNeg T Cells


title: Pt010_PBMC

library_source: transcriptomic single cell

value: PBMCs


title: Pt010_CARNeg


title: Pt011_CARPos

value: CARPos T Cells


title: Pt009_PBMC


title: Pt009_Product


title: Pt008_CARNeg


title: Pt008_Product


title: Pt008_CARPos


title: Pt007_CARPos


title: Pt007_PBMC


title: Pt007_CARNeg


title: Pt006_PBMC


title: Pt007_Product

value: CAR T Cells


title: Pt006_CARNeg


title: Pt011_PBMC


title: Pt006_CARPos


title: 02 WT Treg cells, spleen


title: H2O2_ARB_3

city: Tianji

first: Ling

last: Wang

address: No. 22 Qixiang Tai Road, Heping District

institute: Clinical College of Ophthalmology, Tianjin Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: visual organo

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: visual organo

value: human retinal pigmental epithelial cell (ARPE-19)


title: H2O2_ARB_2


title: H2O2_ARB_1


title: H2O2_3


title: H2O2_2


title: H2O2_1


title: Pt009_CARNeg


title: hepg2_55_sgRNA

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 55
hepg2_raw_singlecell_01.h5ad

data_processing:
The demultiplexing, barcoded processing, and gene counting were conducted using Cell Ranger software v4.0.0 count function.
reference genome: 10x genomics refdata-gex-GRCh38-2020-A
Assembly: GRCh38
Supplementary files format and content: AnnData format where the .var annotation details genes while the .obs annotation details single-cells.
Supplementary files format and content: Data is saved in .h5ad format.

growth_protocol: See Nadiq et al. 2024

extract_protocol:
See Nadiq et al. 2024
10x Genomics 3' v3 user guide CG000184 Rev C

treatment_protocol: See Nadiq et al. 2024

value: day 7 post transduction


title: Pt010_Product


title: hepg2_53_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 53
hepg2_raw_singlecell_01.h5ad


title: hepg2_52_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 52
hepg2_raw_singlecell_01.h5ad


title: hepg2_56_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 56
hepg2_raw_singlecell_01.h5ad


title: Pt008_PBMC


title: hepg2_54_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 54
hepg2_raw_singlecell_01.h5ad


title: hepg2_47_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 47
hepg2_raw_singlecell_01.h5ad


title: hepg2_50_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 50
hepg2_raw_singlecell_01.h5ad


title: hepg2_49_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 49
hepg2_raw_singlecell_01.h5ad


title: hepg2_46_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 46
hepg2_raw_singlecell_01.h5ad


title: hepg2_44_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 44
hepg2_raw_singlecell_01.h5ad


title: hepg2_43_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 43
hepg2_raw_singlecell_01.h5ad


title: hepg2_42_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 42
hepg2_raw_singlecell_01.h5ad


title: hepg2_41_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 41
hepg2_raw_singlecell_01.h5ad


title: hepg2_38_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 38
hepg2_raw_singlecell_01.h5ad


title: hepg2_40_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 40
hepg2_raw_singlecell_01.h5ad


title: hepg2_39_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 39
hepg2_raw_singlecell_01.h5ad


title: hepg2_37_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 37
hepg2_raw_singlecell_01.h5ad


title: hepg2_35_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 35
hepg2_raw_singlecell_01.h5ad


title: hepg2_36_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 36
hepg2_raw_singlecell_01.h5ad


title: hepg2_31_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 31
hepg2_raw_singlecell_01.h5ad


title: hepg2_30_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 30
hepg2_raw_singlecell_01.h5ad


title: hepg2_32_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 32
hepg2_raw_singlecell_01.h5ad


title: hepg2_33_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 33
hepg2_raw_singlecell_01.h5ad


title: hepg2_34_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 34
hepg2_raw_singlecell_01.h5ad


title: hepg2_26_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 26
hepg2_raw_singlecell_01.h5ad


title: hepg2_29_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 29
hepg2_raw_singlecell_01.h5ad


title: hepg2_27_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 27
hepg2_raw_singlecell_01.h5ad


title: hepg2_24_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 24
hepg2_raw_singlecell_01.h5ad


title: hepg2_28_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 28
hepg2_raw_singlecell_01.h5ad


title: hepg2_51_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 51
hepg2_raw_singlecell_01.h5ad


title: hepg2_45_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 45
hepg2_raw_singlecell_01.h5ad


title: hepg2_23_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 23
hepg2_raw_singlecell_01.h5ad


title: hepg2_48_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 48
hepg2_raw_singlecell_01.h5ad


title: hepg2_21_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 21
hepg2_raw_singlecell_01.h5ad


title: hepg2_25_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 25
hepg2_raw_singlecell_01.h5ad


title: hepg2_19_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 19
hepg2_raw_singlecell_01.h5ad


title: hepg2_18_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 18
hepg2_raw_singlecell_01.h5ad


title: hepg2_20_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 20
hepg2_raw_singlecell_01.h5ad


title: hepg2_17_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 17
hepg2_raw_singlecell_01.h5ad


title: hepg2_13_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 13
hepg2_raw_singlecell_01.h5ad


title: hepg2_10_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 10
hepg2_raw_singlecell_01.h5ad


title: hepg2_9_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 9
hepg2_raw_singlecell_01.h5ad


title: hepg2_12_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 12
hepg2_raw_singlecell_01.h5ad


title: hepg2_22_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 22
hepg2_raw_singlecell_01.h5ad


title: hepg2_11_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 11
hepg2_raw_singlecell_01.h5ad


title: hepg2_8_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 8
hepg2_raw_singlecell_01.h5ad


title: hepg2_4_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 4
hepg2_raw_singlecell_01.h5ad


title: hepg2_5_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 5
hepg2_raw_singlecell_01.h5ad


title: hepg2_2_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 2
hepg2_raw_singlecell_01.h5ad


title: hepg2_1_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 1
hepg2_raw_singlecell_01.h5ad


title: hepg2_3_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 3
hepg2_raw_singlecell_01.h5ad


title: jurkat_56_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 56
jurkat_raw_singlecell_01.h5ad

source_name: Jurkat

value: Jurkat


title: jurkat_51_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 51
jurkat_raw_singlecell_01.h5ad


title: hepg2_16_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 16
hepg2_raw_singlecell_01.h5ad


title: jurkat_53_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 53
jurkat_raw_singlecell_01.h5ad


title: jurkat_49_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 49
jurkat_raw_singlecell_01.h5ad


title: hepg2_15_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 15
hepg2_raw_singlecell_01.h5ad


title: jurkat_52_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 52
jurkat_raw_singlecell_01.h5ad


title: jurkat_54_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 54
jurkat_raw_singlecell_01.h5ad


title: jurkat_50_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 50
jurkat_raw_singlecell_01.h5ad


title: hepg2_14_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 14
hepg2_raw_singlecell_01.h5ad


title: hepg2_7_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 7
hepg2_raw_singlecell_01.h5ad


title: jurkat_55_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 55
jurkat_raw_singlecell_01.h5ad


title: hepg2_6_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 6
hepg2_raw_singlecell_01.h5ad


title: jurkat_44_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 44
jurkat_raw_singlecell_01.h5ad


title: jurkat_45_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 45
jurkat_raw_singlecell_01.h5ad


title: jurkat_47_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 47
jurkat_raw_singlecell_01.h5ad


title: jurkat_43_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 43
jurkat_raw_singlecell_01.h5ad


title: jurkat_48_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 48
jurkat_raw_singlecell_01.h5ad


title: jurkat_46_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 46
jurkat_raw_singlecell_01.h5ad


title: jurkat_42_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 42
jurkat_raw_singlecell_01.h5ad


title: jurkat_41_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 41
jurkat_raw_singlecell_01.h5ad


title: jurkat_40_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 40
jurkat_raw_singlecell_01.h5ad


title: jurkat_39_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 39
jurkat_raw_singlecell_01.h5ad


title: jurkat_35_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 35
jurkat_raw_singlecell_01.h5ad


title: jurkat_38_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 38
jurkat_raw_singlecell_01.h5ad


title: jurkat_36_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 36
jurkat_raw_singlecell_01.h5ad


title: jurkat_34_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 34
jurkat_raw_singlecell_01.h5ad


title: jurkat_37_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 37
jurkat_raw_singlecell_01.h5ad


title: jurkat_33_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 33
jurkat_raw_singlecell_01.h5ad


title: jurkat_32_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 32
jurkat_raw_singlecell_01.h5ad


title: jurkat_31_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 31
jurkat_raw_singlecell_01.h5ad


title: jurkat_29_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 29
jurkat_raw_singlecell_01.h5ad


title: jurkat_28_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 28
jurkat_raw_singlecell_01.h5ad


title: jurkat_27_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 27
jurkat_raw_singlecell_01.h5ad


title: jurkat_26_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 26
jurkat_raw_singlecell_01.h5ad


title: jurkat_24_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 24
jurkat_raw_singlecell_01.h5ad


title: jurkat_23_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 23
jurkat_raw_singlecell_01.h5ad


title: jurkat_30_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 30
jurkat_raw_singlecell_01.h5ad


title: jurkat_20_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 20
jurkat_raw_singlecell_01.h5ad


title: jurkat_19_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 19
jurkat_raw_singlecell_01.h5ad


title: jurkat_18_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 18
jurkat_raw_singlecell_01.h5ad


title: jurkat_25_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 25
jurkat_raw_singlecell_01.h5ad


title: jurkat_21_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 21
jurkat_raw_singlecell_01.h5ad


title: jurkat_16_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 16
jurkat_raw_singlecell_01.h5ad


title: jurkat_12_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 12
jurkat_raw_singlecell_01.h5ad


title: jurkat_22_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 22
jurkat_raw_singlecell_01.h5ad


title: jurkat_10_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 10
jurkat_raw_singlecell_01.h5ad


title: jurkat_9_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 9
jurkat_raw_singlecell_01.h5ad


title: jurkat_15_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 15
jurkat_raw_singlecell_01.h5ad


title: jurkat_7_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 7
jurkat_raw_singlecell_01.h5ad


title: jurkat_6_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 6
jurkat_raw_singlecell_01.h5ad


title: jurkat_5_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 5
jurkat_raw_singlecell_01.h5ad


title: jurkat_4_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 4
jurkat_raw_singlecell_01.h5ad


title: jurkat_2_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 2
jurkat_raw_singlecell_01.h5ad


title: hepg2_56_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 56
hepg2_raw_singlecell_01.h5ad


title: hepg2_54_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 54
hepg2_raw_singlecell_01.h5ad


title: hepg2_55_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 55
hepg2_raw_singlecell_01.h5ad


title: hepg2_51_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 51
hepg2_raw_singlecell_01.h5ad


title: jurkat_3_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 3
jurkat_raw_singlecell_01.h5ad


title: hepg2_53_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 53
hepg2_raw_singlecell_01.h5ad


title: jurkat_17_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 17
jurkat_raw_singlecell_01.h5ad


title: jurkat_14_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 14
jurkat_raw_singlecell_01.h5ad


title: jurkat_13_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 13
jurkat_raw_singlecell_01.h5ad


title: hepg2_50_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 50
hepg2_raw_singlecell_01.h5ad


title: hepg2_48_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 48
hepg2_raw_singlecell_01.h5ad


title: hepg2_49_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 49
hepg2_raw_singlecell_01.h5ad


title: hepg2_46_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 46
hepg2_raw_singlecell_01.h5ad


title: hepg2_47_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 47
hepg2_raw_singlecell_01.h5ad


title: jurkat_1_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 1
jurkat_raw_singlecell_01.h5ad


title: hepg2_45_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 45
hepg2_raw_singlecell_01.h5ad


title: hepg2_52_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 52
hepg2_raw_singlecell_01.h5ad


title: hepg2_44_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 44
hepg2_raw_singlecell_01.h5ad


title: jurkat_11_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 11
jurkat_raw_singlecell_01.h5ad


title: hepg2_43_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 43
hepg2_raw_singlecell_01.h5ad


title: hepg2_41_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 41
hepg2_raw_singlecell_01.h5ad


title: jurkat_8_sgRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 8
jurkat_raw_singlecell_01.h5ad


title: hepg2_42_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 42
hepg2_raw_singlecell_01.h5ad


title: hepg2_40_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 40
hepg2_raw_singlecell_01.h5ad


title: hepg2_39_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 39
hepg2_raw_singlecell_01.h5ad


title: hepg2_38_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 38
hepg2_raw_singlecell_01.h5ad


title: hepg2_36_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 36
hepg2_raw_singlecell_01.h5ad


title: hepg2_35_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 35
hepg2_raw_singlecell_01.h5ad


title: hepg2_34_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 34
hepg2_raw_singlecell_01.h5ad


title: hepg2_27_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 27
hepg2_raw_singlecell_01.h5ad


title: hepg2_31_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 31
hepg2_raw_singlecell_01.h5ad


title: hepg2_29_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 29
hepg2_raw_singlecell_01.h5ad


title: hepg2_33_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 33
hepg2_raw_singlecell_01.h5ad


title: hepg2_30_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 30
hepg2_raw_singlecell_01.h5ad


title: hepg2_32_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 32
hepg2_raw_singlecell_01.h5ad


title: hepg2_28_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 28
hepg2_raw_singlecell_01.h5ad


title: hepg2_24_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 24
hepg2_raw_singlecell_01.h5ad


title: hepg2_25_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 25
hepg2_raw_singlecell_01.h5ad


title: hepg2_19_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 19
hepg2_raw_singlecell_01.h5ad


title: hepg2_18_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 18
hepg2_raw_singlecell_01.h5ad


title: hepg2_26_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 26
hepg2_raw_singlecell_01.h5ad


title: hepg2_16_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 16
hepg2_raw_singlecell_01.h5ad


title: hepg2_22_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 22
hepg2_raw_singlecell_01.h5ad


title: hepg2_23_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 23
hepg2_raw_singlecell_01.h5ad


title: hepg2_21_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 21
hepg2_raw_singlecell_01.h5ad


title: hepg2_17_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 17
hepg2_raw_singlecell_01.h5ad


title: hepg2_15_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 15
hepg2_raw_singlecell_01.h5ad


title: hepg2_14_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 14
hepg2_raw_singlecell_01.h5ad


title: hepg2_13_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 13
hepg2_raw_singlecell_01.h5ad


title: hepg2_11_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 11
hepg2_raw_singlecell_01.h5ad


title: hepg2_12_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 12
hepg2_raw_singlecell_01.h5ad


title: hepg2_10_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 10
hepg2_raw_singlecell_01.h5ad


title: hepg2_9_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 9
hepg2_raw_singlecell_01.h5ad


title: hepg2_37_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 37
hepg2_raw_singlecell_01.h5ad


title: hepg2_8_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 8
hepg2_raw_singlecell_01.h5ad


title: hepg2_6_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 6
hepg2_raw_singlecell_01.h5ad


title: hepg2_7_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 7
hepg2_raw_singlecell_01.h5ad


title: hepg2_20_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 20
hepg2_raw_singlecell_01.h5ad


title: hepg2_5_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 5
hepg2_raw_singlecell_01.h5ad


title: hepg2_4_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 4
hepg2_raw_singlecell_01.h5ad


title: hepg2_3_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 3
hepg2_raw_singlecell_01.h5ad


title: hepg2_2_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 2
hepg2_raw_singlecell_01.h5ad


title: hepg2_1_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale HepG2 Perturb-seq experiment, gemgroup 1
hepg2_raw_singlecell_01.h5ad


title: jurkat_56_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 56
jurkat_raw_singlecell_01.h5ad


title: jurkat_55_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 55
jurkat_raw_singlecell_01.h5ad


title: jurkat_52_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 52
jurkat_raw_singlecell_01.h5ad


title: jurkat_48_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 48
jurkat_raw_singlecell_01.h5ad


title: jurkat_54_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 54
jurkat_raw_singlecell_01.h5ad


title: jurkat_51_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 51
jurkat_raw_singlecell_01.h5ad


title: jurkat_49_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 49
jurkat_raw_singlecell_01.h5ad


title: jurkat_50_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 50
jurkat_raw_singlecell_01.h5ad


title: jurkat_44_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 44
jurkat_raw_singlecell_01.h5ad


title: jurkat_41_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 41
jurkat_raw_singlecell_01.h5ad


title: jurkat_53_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 53
jurkat_raw_singlecell_01.h5ad


title: jurkat_39_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 39
jurkat_raw_singlecell_01.h5ad


title: jurkat_46_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 46
jurkat_raw_singlecell_01.h5ad


title: jurkat_45_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 45
jurkat_raw_singlecell_01.h5ad


title: jurkat_38_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 38
jurkat_raw_singlecell_01.h5ad


title: jurkat_40_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 40
jurkat_raw_singlecell_01.h5ad


title: jurkat_36_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 36
jurkat_raw_singlecell_01.h5ad


title: jurkat_35_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 35
jurkat_raw_singlecell_01.h5ad


title: jurkat_43_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 43
jurkat_raw_singlecell_01.h5ad


title: jurkat_34_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 34
jurkat_raw_singlecell_01.h5ad


title: jurkat_33_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 33
jurkat_raw_singlecell_01.h5ad


title: jurkat_31_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 31
jurkat_raw_singlecell_01.h5ad


title: jurkat_37_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 37
jurkat_raw_singlecell_01.h5ad


title: jurkat_47_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 47
jurkat_raw_singlecell_01.h5ad


title: jurkat_32_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 32
jurkat_raw_singlecell_01.h5ad


title: jurkat_28_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 28
jurkat_raw_singlecell_01.h5ad


title: jurkat_27_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 27
jurkat_raw_singlecell_01.h5ad


title: jurkat_42_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 42
jurkat_raw_singlecell_01.h5ad


title: jurkat_26_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 26
jurkat_raw_singlecell_01.h5ad


title: jurkat_29_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 29
jurkat_raw_singlecell_01.h5ad


title: jurkat_24_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 24
jurkat_raw_singlecell_01.h5ad


title: jurkat_30_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 30
jurkat_raw_singlecell_01.h5ad


title: jurkat_22_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 22
jurkat_raw_singlecell_01.h5ad


title: jurkat_19_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 19
jurkat_raw_singlecell_01.h5ad


title: jurkat_20_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 20
jurkat_raw_singlecell_01.h5ad


title: jurkat_21_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 21
jurkat_raw_singlecell_01.h5ad


title: TE A9

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

description: TEAD4-/- D8 in vitro produced bovine blastocyst

data_processing:
Paired-end read fastq files were quality checked with FastQC (Andrews, 2010) and preprocessed with fastp (Chen et al., 2018). Resulting files were pseudoaligned and quantified using kallisto (Bray et al., 2016) against the reference transcriptome of Bos taurus ARS.UCD1.2 (Ensembl release 109).
Assembly: Bos taurus ARS.UCD1.2 (Ensembl 109)
Supplementary files format and content: Comma text file with TPM normalized values for each Sample

organism: Bos taurus

source_name: ICM+TE blastomere

growth_protocol: In vitro culture in droplets of synthetic oviduct fluid at 38.5ºC in an atmosphere with 5% CO2, 5% O2, 90% N2 with maximum humidity.

extract_protocol:
Total RNA was extracted using MagMAX mirVana Total Isolation Kit (Applied Biosystems) following the manufacturer's instruction with minor modifications. Briefly 200 µl of Lysis Binding Mix were added to the sample, followed by gentle pipetting and 5 min incubation at room temperature. Then 20 µl of Binding Beads Mix were added and shaken gently for 5 min. Beads‐mRNA complexes were washed once in each Wash Solution 1 and 2. Following the washing step, samples were treated with 50 µl of Turbo DNAse treatment, 50 µl of Rebinding Buffer and 100 µl of Isopropanol were added to the sample and mixed gently. Finally, following a double wash in Wash Solution 2, total RNA was eluted in 20 µl of Elution Buffer and stored at −80°C until analysis.
RNA‐seq libraries were prepared with KAPA Stranded mRNA‐Seq Illumina Platforms Kit (Roche) following the manufacturer's recommendations. Briefly, 50–100 ng of total RNA was used for the poly‐A fraction enrichment with oligo‐dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt‐end double stranded cDNA was 3′ adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on a HiSeq. 4000 system (Illumina) with a read length of 2 × 76 bp + 8 bp + 8 bp using the HiSeq. 4000 SBS kit (Illumina) obtaining >30 M reads/sample.

treatment_protocol: Snap freeze and storage at -80ºC

value: ICM+TE blastomere


title: jurkat_18_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 18
jurkat_raw_singlecell_01.h5ad


title: jurkat_17_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 17
jurkat_raw_singlecell_01.h5ad


title: TE A7


title: jurkat_16_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 16
jurkat_raw_singlecell_01.h5ad


title: jurkat_15_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 15
jurkat_raw_singlecell_01.h5ad


title: TE A6


title: jurkat_12_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 12
jurkat_raw_singlecell_01.h5ad


title: jurkat_13_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 13
jurkat_raw_singlecell_01.h5ad


title: jurkat_14_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 14
jurkat_raw_singlecell_01.h5ad


title: jurkat_11_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 11
jurkat_raw_singlecell_01.h5ad


title: jurkat_10_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 10
jurkat_raw_singlecell_01.h5ad


title: WT A5

description: wild type D8 in vitro produced bovine blastocyst


title: jurkat_25_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 25
jurkat_raw_singlecell_01.h5ad


title: jurkat_23_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 23
jurkat_raw_singlecell_01.h5ad


title: WT A4


title: jurkat_8_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 8
jurkat_raw_singlecell_01.h5ad


title: WT A2


title: jurkat_7_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 7
jurkat_raw_singlecell_01.h5ad


title: WT A3


title: TE A8


title: WT A1


title: jurkat_6_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 6
jurkat_raw_singlecell_01.h5ad


title: scRNA_organoid_2month_wt

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
For scRNA-seq data analysis, paired-end reads were aligned to human reference genome (hg38) using Cell Ranger.
Cells with >20% mitochondrial content, <300 features, and features expressed in <3 cells were excluded. Scrublet and gene expression (>40000 counts) detected doublets with default settings and expected rate at 10%.
Data integration was performed on the top highly variable genes via Harmony with default parameters. UMAP was performed on the Harmony-corrected PCA embedding. Louvain clustering was calculated using sc.tl.louvain with a resolution of 1. DEGs for each cell type population were selected by Seurat via FindMarkers with min. pct = 0.25 and adjusted p value < 0.05. GO enrichment analysis was performed using the enrichGO function in the clusterProfiler package.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 2-month cortical organoid derived from wild-type hESC

growth_protocol: Human ESCs were cultured in PGM1 human pluripotent stem cell culture medium  in Matrigel -coated culture plates.

extract_protocol:
The construction process of the scRNA-seq library for cortical organoids was carried out by SequMed Biotech Inc.
Cell suspensions were processed using the DNBelab C Series Single-Cell Library Prep set (MGI),the libraries were sequenced on the DNBSEQ-T7RS platform.

treatment_protocol: CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.

value: 2-month cortical organoid

value: wild type


title: scRNA_organoid_2month_hete

source_name: 2-month cortical organoid derived from CTCF R567W heterozygous hESC

value: CTCF heterozygous mutation


title: hMSC R206H, BYL719, BMP6, 3

city: Oviedo

first: Gonzalo

last: Sánchez-Duffhues

state: Asturias

address: Avda. de Roma, s/n

institute: Nanomaterials and Nanotechnology Research Center (CINN-CSIC)

description: processed counts, column 31

data_processing:
The raw reads were processed by removing adapters, ploy-N and other low quality reads. Subsequent quality control was performed and further down-stream analyses were based on the clean data with high quality.
The clean reads were mapped to the GRCh38/hg38 reference genome using Hisat2 v2.0.5.
The total counts per gene were quantified using featureCounts v1.5.0-p3. These are the processed data supplied in the processed data file matrix.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data file format is .csv and consists of the following columns gene_id, WT1_1, WT1_2, WT1_3, WT1_4, WT2_1, WT2_2, WT2_3, WT2_4, WT3_1, WT3_2, WT3_3, WT3_4, WT5_1, WT5_2, WT5_3, WT5_4, WT6_1, WT6_2, WT6_3, WT6_4, RH1_1, RH1_2, RH1_4, RH2_1, RH2_2, RH2_3, RH2_4, RH3_1, RH3_2, RH3_3, RH3_4, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family

source_name: bone marrow derived

growth_protocol: The hMSCs (overexpressed with ACVR1-WT or -R206H) were cultured in AMEM (Gibco) supplemented with 10% FBS, 1 ng/ml bFGF (ReproTech) and 100U/ml P/S

extract_protocol:
ReliaPrep RNA Miniprep Systems (Promega)
mRNA was purified from tRNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTPs. Subsequent A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification and purification was performed to construct the directional library.

treatment_protocol: Overnight serum starvation was performed with DMEM (Gibco) without any supplements. The cells were pre-treated with 1uM BYL719 or DMSO for 30 minutes in DMEM (Gibco) prior to 1 hour stimulation with Activin A (50 ng/ml) or BMP6 (50 ng/ml) (both R&D).

value: bone marrow derived

value: hMSC

value: transduced ACVR1-R206H

value: BYL719, Activin A


title: scRNA_organoid_1month_wt

source_name: 1-month cortical organoid derived from wild-type hESC

value: 1-month cortical organoid


title: hMSC R206H, BYL719, BMP6, 4

description: processed counts, column 32


title: jurkat_4_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 4
jurkat_raw_singlecell_01.h5ad


title: jurkat_5_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 5
jurkat_raw_singlecell_01.h5ad


title: jurkat_2_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 2
jurkat_raw_singlecell_01.h5ad


title: hMSC R206H, BYL719, BMP6, 1

description: processed counts, column 29


title: sparc_atac_brain_homo

data_processing:
library strategy: SPARC-seq
For Spatial-RNA-seq, the data integration of wild-type and mutant samples was performed using “FindIntegrationAnchors” and “IntegrateData”, a module in Seurat v4.0.
For Spatial-ATAC-seq, the data was integrated by using “RunHarmony” a mudule in Harmony v0.1.0. For SPARC-seq data integration, Weighted Nearest Neighbor Analysis was used to integrate the Spatial-RNA-seq profiles and Spatial-ATAC-seq profiles.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tissue from E18.5 mouse embryo

growth_protocol: Mice were housed in a specific pathogen–free (SPF) facility with a 12 h dark/12 h light cycle and provided with food and water ad libitum.

extract_protocol:
SPARC-seq experiments of E18.5 brain samples were performed according to previously described.
The cDNA library construction was performed according to the manufacturer’s guidelines of TruePrep DNA Library Prep Kit V2 for Illumina.

value: brain tissue from E18.5 mouse embryo

value: Ctcf homozygous mutation


title: BHLKO, replicate 3, scRNAseq

city: Houston

first: Rachel

last: Van Drunen

state: TX

address: Pressler

institute: MD Anderson University of Texas Health Science Center Houston

description: 10X Genomics

data_processing:
Cell Ranger was used for filtering, gene counting and aggregations. STAR alignment was used to align the reads to the mouse transcriptome reference (mm10, Ensembl 93) including introns model
Assembly: mm10
Supplementary files format and content: H5

source_name: Lung

extract_protocol:
The whole lung of BHLKO male mice and AlbCRE male mice for control were collected at CT4. Three biological replicates were taken for each condition so a total of six lungs were used. The steps for dissociation were followed according to the Miltenyi Biotec lung dissociation kit protocol (#130-095-927). In short, the lungs were dissociated using enzymatic degradation followed by gentleMACs dissociation (#130-093-235) to obtain single cell suspension.
Cells were counted and diluted to a final concentration in PBS supplemented with 0.04% BSA. Cellular suspension was loaded onto Next GEM Chip G at a concentration of 700-1200 cells/µL and then ran on a Chromium X instrument to generate GEM emulsion (10x Genomics). Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3.1 Chemistry).

value: Lung

tag: Sex

value: male

value: BHLKO


title: jurkat_9_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 9
jurkat_raw_singlecell_01.h5ad


title: BHLKO, replicate 2, scRNAseq

description: 10X Genomics


title: hMSC R206H, DMSO, BMP6, 3

description: processed counts, column 27

value: DMSO, Activin A


title: jurkat_3_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 3
jurkat_raw_singlecell_01.h5ad

value: day 7 post transduction


title: sparc_rna_brain_homo


title: hMSC R206H, DMSO, BMP6, 4

description: processed counts, column 28


title: BHLKO, replicate 1, scRNAseq

description: 10X Genomics


title: jurkat_1_mRNA

description:
3' scRNA-seq
10x Genomics
Essential-scale Jurkat Perturb-seq experiment, gemgroup 1
jurkat_raw_singlecell_01.h5ad

value: Jurkat


title: AlbCre, replicate 3, scRNAseq

description: 10X Genomics

value: AlbCRE


title: hMSC R206H, DMSO, BMP6, 2

description: processed counts, column 26


title: hMSC R206H, DMSO, BMP6, 1

description: processed counts, column 25


title: AlbCre, replicate 2, scRNAseq

description: 10X Genomics


title: hMSC R206H, DMSO, Vehicle, 4

description: processed counts, column 24

value: DMSO, Vehicle


title: AlbCre, replicate 1, scRNAseq

description: 10X Genomics


title: hMSC R206H, DMSO, Vehicle, 1

description: processed counts, column 22


title: hMSC R206H, DMSO, Vehicle, 2

description: processed counts, column 23


title: scRNA_organoid_1month_hete

source_name: 1-month cortical organoid derived from CTCF R567W heterozygous hESC


title: hMSC R206H, BYL719, BMP6, 2

description: processed counts, column 30


title: hMSC WT, BYL719, Activin A, 4

description: processed counts, column 21

value: transduced ACVR1-WT


title: hMSC WT, BYL719, Activin A, 3

description: processed counts, column 20


title: hMSC WT, BYL719, Activin A, 2

description: processed counts, column 19


title: hMSC WT, BYL719, Activin A, 1

description: processed counts, column 18


title: hMSC WT, DMSO, Activin A, 4

description: processed counts, column 17


title: hMSC WT, DMSO, Activin A, 3

description: processed counts, column 16


title: hMSC WT, DMSO, Activin A, 2

description: processed counts, column 15


title: hMSC WT, BYL719, BMP6, 4

description: processed counts, column 13

value: BYL719, BMP6


title: LV_cKO_F_rep3

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

data_processing:
Reads underwent initial quality check with FastQC v0.74, then quality filtering and adapter trimming was conducted with Cutadapt v4.6.
Filtered reads were aligned using STAR v2.7.11a in 2-pass mode.
Gene expression was quantified at the gene level using HTseq-counts v2.0.5 and collated into a counts matrix
Assembly: GRCm39.104
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Left ventricle

growth_protocol: Mice were housed in a temperature-controlled environment with a 12-hour light/dark cycle and fed standard chow ad libitum. Tissue was collected at 12-16 weeks of age, following 2 weeks of saline infusion via implanted osmotic minipump.

extract_protocol:
Left ventricle tissue (~20 mg) was mechanically homogenised in TRI reagent with a 5 mm steel bead at 30 Hz for 2 x 30 s (TissueLyser II, Qiagen) then centrifuged for 10 min at 10,000 x g. RNA was extracted from the supernatant using spin columns with DNase-I treatment (Zymo DirectZol RNA Miniprep kit #R2050, Integrated Sciences, Australia). RNA concentration and purity was determined spectrophotometrically (Nanodrop, Thermo Fisher, Australia) and RNA integrity number (RIN) was determined by electrophoresis (Tapestation, Agilent). All sample RIN values were ≥7.7.
Stranded libraries were prepared from 500 ng total RNA input with poly-A+ selection (TruSeq Stranded mRNA, Illumina) following manufacturer's protocols

value: cardiomyocyte-specific Ppp2r2a knockout (aMHC-CreTg/0-Ppp2r2aL/L)

value: Left ventricle

value: Female


title: LV_cKO_F_rep2


title: LV_Ctrl_F_rep5

value: floxed control (aMHC-Cre0/0-Ppp2r2aL/L)


title: LV_cKO_F_rep6


title: LV_cKO_F_rep7


title: LV_cKO_F_rep5


title: LV_cKO_F_rep1


title: hMSC WT, DMSO, Activin A, 1

description: processed counts, column 14

value: bone marrow derived

value: hMSC


title: LV_Ctrl_F_rep3


title: LV_Ctrl_F_rep6


title: LV_Ctrl_F_rep4


title: hMSC WT, BYL719, BMP6, 2

description: processed counts, column 11


title: LV_Ctrl_F_rep1


title: hMSC WT, BYL719, BMP6, 1

description: processed counts, column 10


title: LV_Ctrl_F_rep2


title: hMSC WT, BYL719, BMP6, 3

description: processed counts, column 12


title: LV_cKO_M_rep7

value: Male


title: hMSC WT, DMSO, BMP6, 4

description: processed counts, column 9

value: DMSO, BMP6


title: LV_cKO_M_rep5


title: LV_cKO_F_rep4


title: hMSC WT, DMSO, BMP6, 3

description: processed counts, column 8


title: hMSC WT, DMSO, BMP6, 2

description: processed counts, column 7


title: hMSC WT, DMSO, BMP6, 1

description: processed counts, column 6


title: LV_cKO_M_rep6


title: LV_cKO_M_rep1


title: hMSC WT, DMSO, Vehicle, 3

description: processed counts, column 4


title: LV_Ctrl_M_rep5


title: LV_Ctrl_M_rep4


title: LV_cKO_M_rep3


title: hMSC WT, DMSO, Vehicle, 1

description: processed counts, column 2


title: PBMC, NoDex, patient 94, bulkRNAseq

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

data_processing:
Gene counts were generated using the nf-core rnaseq pipeline v3.3
Salmon-generated counts were used for analysis
Assembly: GRCh38
Supplementary files format and content: CSV file including Salmon-generated raw counts

source_name: PBMC

extract_protocol:
RNA was extracted from 2.5 x 105 PBMCs using the Quick-RNA MagBead Kit (Zymo) with DNase digestion
RNA quality was assessed using a Fragment Analyzer (Agilent) and 10ng RNA was used to synthesize full length cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). The cDNA was purified using bead cleanup, followed by library preparation. Libraries were validated on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 (Emory) at 100 bp paired-end read length targeting ~25 million reads per sample. using Nextera XT kit (Illumina).

treatment_protocol: The Dex group received at least one dose of 6mg dexamethasone at the time of initial biosampling

value: PBMC

tag: study days

value: NoDex


title: PBMC, Dex, patient 350, bulkRNAseq

value: Dex


title: PBMC, Dex, patient 271, bulkRNAseq


title: PBMC, Dex, patient 340, bulkRNAseq


title: hMSC WT, DMSO, Vehicle, 4

description: processed counts, column 5

tag: cell line


title: PBMC, Dex, patient 254, bulkRNAseq


title: LV_Ctrl_M_rep6


title: LV_cKO_M_rep2


title: hMSC WT, DMSO, Vehicle, 2

description: processed counts, column 3

tag: cell type


title: LV_Ctrl_M_rep3


title: LV_Ctrl_M_rep2


title: PBMC, Dex, patient 276, bulkRNAseq


title: snRNA_cortex_homo

data_processing:
For snRNA-seq data analysis, the BD Rhapsody whole transcriptome analysis (WTA) pipeline was utilized to process FASTQ files, converting raw sequencing reads into gene expression matrix with unique molecular identifier (UMI) counts for each gene in each cell.
The Seurat was utilized for further analysis of the read count matrix for each gene/sample. Quality control measures were applied to filter individual cells, retaining only those expressing genes detected in at least 3 cells and cells expressing a minimum of 200 genes. Additionally, cells with gene expression counts ranging from 500 to 6000, mitochondrial gene expression not exceeding 20%, and a minimum RNA count of 2000 per cell were retained.
For cell annotation, the ScType package was used. To identify  differential expression genes, the Seurat package's FindMarkers function was employed. differential expression analysis utilized the Wilcox method, which applies the Wilcoxon rank-sum test to compare gene expression levels between groups of cells. Benjamini-Hochberg method was used for multiple testing correction of p-values to ensure the rigour of the statistical results. A corrected p-value less than 0.05 with log2Foldchange above 0.5 was considered statistically significant.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cortex tissue from E18.5 mouse embryo

extract_protocol:
SnRNA-seq experiments for E18.5 cortex tissues were performed by SequMed Biotech Inc.
Libraries were constructed according to instruction manual of the BD Rhapsody WTA Amplification kit  on BD Rhapsody system.
snRNA-seq

value: cortex tissue from E18.5 mouse embryo

value: Ctcf homozygous mutation


title: PBMC, Dex, patient 253, bulkRNAseq


title: PBMC, Dex, patient 238, bulkRNAseq


title: LV_cKO_M_rep4


title: PBMC, Dex, patient 156, bulkRNAseq


title: YCKO_3

city: changchun

first: lei

last: shi

address: changchun

institute: jilin university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing Nbase and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs equenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly differential expression.
Assembly: mouse reference genome(GRCm38.p6)
Supplementary files format and content: Processed data files; txt; fpkm of each gene

source_name: Heart

extract_protocol:
Ythdc1flox/flox and Ythdc1-CKO mice were fed with normal chow for 15 days.Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction uffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: Heart


title: PBMC, Dex, patient 154, bulkRNAseq


title: YCKO_2


title: YCKO_1


title: YFF_3


title: LV_Ctrl_M_rep1


title: YFF_2


title: PBMC, NoDex, patient 107, bulkRNAseq


title: snRNA_cortex_wt

value: wild type


title: hMSC R206H, BYL719, Activin A, 2

data_processing:
The raw reads were processed by removing adapters, ploy-N and other low quality reads. Subsequent quality control was performed and further down-stream analyses were based on the clean data with high quality.
The clean reads were mapped to the GRCh38/hg38 reference genome using Hisat2 v2.0.5.
The total counts per gene were quantified using featureCounts v1.5.0-p3. These are the processed data supplied in the processed data file matrix.
Assembly: GRCh38/hg38
Supplementary files format and content: The processed data file format is .csv and consists of the following columns gene_id, RH5_1, RH5_2, RH5_3, RH5_4, RH6_1, RH6_2, RH6_3, RH6_4, gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family

growth_protocol: The hMSCs were cultured in AMEM (Gibco) supplemented with 10% FBS, 1 ng/ml bFGF (ReproTech) and 100U/ml P/S

treatment_protocol: Overnight serum starvation was performed with DMEM (Gibco) without any supplements. The cells were pre-treated with 1uM BYL719 or DMSO for 30 minutes in DMEM (Gibco) prior to 1 hour stimulation with Activin A (50 ng/ml) (R&D).

value: transduced ACVR1-R206H

value: BYL719, Activin A


title: hMSC R206H, BYL719, Activin A, 3


title: YKO

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Peaks were merged with ‘bedtoolsmerge’ for differential peak analysis. Differential peak calling was performed using our own R script. Only peaks with foldchange more than 0.5 were considered as differential peaks. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Assembly: Ensemble_GRCm38.p6
Supplementary files format and content: YKO_vs_YFF_peak_compare_table.txt

extract_protocol:
Nuclei was extracted from heart samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Ythdc1flox/flox and Ythdc1CKO mice were fed with normal chow diet for 15 days old

value: Ythdc1 CKO


title: snRNA_lung_wt

data_processing:
library strategy: snRNA-seq
For snRNA-seq data analysis, paired-end reads were aligned to mouse reference genome (mm10) using Cell Ranger.
Raw count matrices were used to remove ambient RNA with SoupX, then analyzed using Seurat. Poor quality cells were filtered out. Potential doublets were removed with DoubletFinder.
The data was then normalized and integrated using SCTransform integration workflow by regressing out cell cycle effect and percentages of mitochondria-expressed genes per cell. Principal component analysis (PCA) was performed, dimensionality reduction (UMAP) and clustering were then carried out. Cell markers for each cell cluster were determined with FindAllMarkers function.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung tissue from E18.5 mouse embryo

extract_protocol:
SnRNA-seq experiments for E18.5 heart and lung tissues were performed by Jiayin Biotechnology Ltd.
Libraries were constructed according to instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 with 10 x Genomics platform.

value: lung tissue from E18.5 mouse embryo


title: snRNA_lung_homo


title: hMSC R206H, DMSO, Activin A, 3

value: DMSO, Activin A


title: snRNA_heart_homo

source_name: heart tissue from E18.5 mouse embryo

value: heart tissue from E18.5 mouse embryo


title: hMSC R206H, DMSO, Activin A, 2

value: bone marrow derived


title: YFF


title: hMSC R206H, DMSO, Activin A, 4

value: hMSC


title: hMSC R206H, DMSO, Activin A, 1


title: gmjmj1920-2 leaf RNA-seq, rep1

first: Chenjiang

last: You

state: Shanghai

data_processing:
Paired reads were trimmed by cutadapt v4.2 and then mapped to the soybean genome Wm82.a2 using STAR v2.7.10b with parameters "--alignIntronMax 5000 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Read pairs mapped to coding transcripts were counted by featureCounts v2.0.3 with parameters "-p --countReadPairs -B -C -O".
Assembly: Wm82.a2.v1
Supplementary files format and content: Tab-delimited txt files containing gene accession, raw read counts, and gene length.

organism: Glycine max

source_name: Leaf

growth_protocol: 12 hr light/12 hr dark, 25˚C

extract_protocol:
Total RNA was isolated from 17-day-old leaves using RN38 Reagent (Aidlab Biotechnologies Co.,Ltd) according to the manufacturer’s instructions. 4 ug of DNase-treated total RNA was used for the construction of sequencing libraries.
Polyadenylated RNA isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) was subjected to RNA-seq library construction with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420L).

value: Leaf

value: somatic cells

value: jmj19 jmj20


title: snRNA_heart_wt


title: W82 leaf RNA-seq, rep1

value: Williams 82


title: PBMC, Dex, patient 419, bulkRNAseq

value: PBMC

tag: disease state

value: severely ill COVID-19 patient

value: Dex


title: gmjmj1920-2 leaf RNA-seq, rep2

tag: genotype


title: JMJ20-OE leaf ChIP-seq input, rep2

data_processing:
Paired reads were trimmed by cutadapt v4.2 and then mapped to the Arabidopsis genome Wm82.a2 using Bowtie2 v2.4.5 with default parameters.
Peak calling was performed by Genrich with parameters "-r -a 200 -p 0.01".
Assembly: Wm82.a2.v1
Supplementary files format and content: bigWig files describing genome coverage of mapped reads

source_name: 17-day-old leaf

extract_protocol:
DNA was extracted from 17-day-old leaves following ChIP assay.
DNA  was subjected to ChIP-seq library construction with VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme #ND607) and VAHTS Multiplex Oligos Set 4/5 for Illumina (Vazyme #N321)

value: 17-day-old leaf

tag: antibody

value: none; input


title: JMJ20-OE leaf ChIP-seq input, rep1


title: PBMC, NoDex, patient 78, bulkRNAseq

value: NoDex


title: W82 leaf RNA-seq, rep2


title: JMJ20-OE leaf ChIP-seq anti-FLAG, rep2

value: anti-FLAG


title: RNAseq_neuron_homo_rep3

data_processing:
Paired-end reads were handled with Trim Galore, and then mapped to mouse (mm10) or human (hg38) genome using STAR aligner.
Transcript abundance were quantified using RSEM. To remove the effect of gender on gene expression in mouse tissue and neural samples, genes originated from ChrX, ChrY were filtered out. Differentially expressed genes (DEGs) were determined using DESeq2.
Assembly: mm10, hg38
Supplementary files format and content: Tab-delimited text files include normalized count values from DESeq2.

source_name: Cultured neurons (2 weeks in vitro) from E18.5 mouse embryo cortex

extract_protocol:
Total RNAs from each mouse tissue or cells were extracted, and were purified with two rounds of mRNA purification with mRNA capture beads to ensure removal of rRNA.
RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina, and the method was performed according to the manufacturer's instructions.

value: Ctcf homozygous mutated


title: hMSC R206H, BYL719, Activin A, 4

value: transduced ACVR1-R206H

value: BYL719, Activin A


title: RNAseq_neuron_homo_rep1

value: Cultured neurons (2 weeks in vitro) from E18.5 mouse embryo cortex


title: YFF_1

value: Heart


title: hMSC R206H, BYL719, Activin A, 1

value: bone marrow derived

value: hMSC


title: PBMC, NoDex, patient 77, bulkRNAseq


title: jmj H3 CUT&Tag rep2

data_processing:
library strategy: CUT&Tag
Paired reads were trimmed by cutadapt v4.2 and then mapped to the Arabidopsis genome Wm82.a2 using Bowtie2 v2.4.5 with default parameters.
Peak calling was performed by Genrich with parameters "-r -a 200 -p 0.01".
Assembly: Wm82.a2.v1
Supplementary files format and content: bigWig files describing genome coverage of mapped reads

extract_protocol:
DNA was extracted from 17-day-old leaves using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme #TD903) according to the manufacturer’s instructions.
DNA was subjected to library construction with TruePrep Index Kit V2 for Illumina (Vazyme #TD202)

value: somatic cells


title: JMJ20-OE leaf ChIP-seq anti-FLAG, rep1


title: RNAseq_neuron_heter_rep3

value: Ctcf heterozygous mutated


title: jmj H3 CUT&Tag rep1

value: jmj19 jmj20


title: PBMC, NoDex, patient 59, bulkRNAseq

value: PBMC


title: PBMC, NoDex, patient 72, bulkRNAseq

value: severely ill COVID-19 patient


title: RNAseq_neuron_heter_rep1


title: jmj H3K36me3 CUT&Tag rep2


title: jmj H3K9me2 CUT&Tag rep2


title: RNAseq_neuron_heter_rep2


title: PBMC, NoDex, patient 43, bulkRNAseq


title: jmj H3K27me3 CUT&Tag rep2


title: RNAseq_neuron_wt_rep3

value: wild type


title: PBMC, NoDex, patient 50, bulkRNAseq


title: jmj H3K36me3 CUT&Tag rep1

value: 17-day-old leaf


title: jmj H3K27me3 CUT&Tag rep1


title: W82 H3 CUT&Tag rep2

value: Williams 82


title: RNAseq_neuron_wt_rep1


title: PBMC, NoDex, patient 2, bulkRNAseq

value: NoDex


title: W82 H3 CUT&Tag rep1


title: W82 H3K9me2 CUT&Tag rep2


title: RNAseq_brain_homo_rep4

value: brain tissue from E18.5 mouse embryo


title: W82 H3K9me2 CUT&Tag rep1


title: W82 H3K4me3 CUT&Tag rep2


title: PBMC, NoDex, patient 1, bulkRNAseq


title: jmj H3K4me3 CUT&Tag rep2


title: RNAseq_brain_homo_rep3

value: Ctcf homozygous mutated


title: jmj H3K9me2 CUT&Tag rep1


title: jmj H3K4me3 CUT&Tag rep1


title: Ku80_CUT&Tag_2

city: Nanning

first: Dandan

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

data_processing:
The paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2
The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools
The filtered reads were then employed to identify CUT&Tag peaks using MACS2
The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR)
Assembly: ToxoDB-57_TgondiiME49 genome
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: tachyzoites

growth_protocol: Transgenic strains were inoculated in 25 cm2 cell culture flasks and washed after 4 h to remove non-invasive parasites. Transgenic strains (1 x 107) were harvested after 20 h of incubation.

extract_protocol:
Library construction was performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina (Novoprotein, Suzhou, China) according to the manufacturer's instructions. Briefly, fresh tachyzoites were bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-HA) at 4°C overnight. After several washes, the parasites were incubated with secondary antibody (1:100, goat anti-mouse IgG) for 1 h at room temperature. The parasites were then resuspended with pAG-Transposome buffer and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by MgCl2 treatment and DNA extraction was performed using DNA extract beads (Novoprotein, Suzhou, China).
Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations (NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina B box, Novoprotein, Suzhou, China).

treatment_protocol: Transgenic parasite strains cultured in Vero cells were treated with either 500 μM IAA or vehicle for 24 h.

value: tachyzoites

value: RH

value: co-culture with DMSO vehicle for 24 h


title: whole-blood, Dex, patient 427, scRNAseq

data_processing:
The BCL files from sequencer were demultiplexed into individual libraries using mkfastqs command in Cellranger 3.0.1 suite of tools (https://support.10xgenomics.com).
The feature-barcode matrices were obtained for each library by aligning the WB raw fastq files to GRCh38 reference genome (annotated with Ensembl v85) and TA raw fastq files to GRCh38 (annotated with Ensembl v85) + SARS-CoV-2 reference genome using default parameters in Cellranger count (v3.0.1).
Assembly: GRCh38 (WB); GRCh38 + SARS-CoV-2 reference genome (TA)
Supplementary files format and content: The count matrices from cellranger are provided as H5 files, the Hierarchical Data Format, that is exported by cellranger-count.

source_name: whole-blood

extract_protocol:
The tracheal aspirate (TA) samples were transported to a BSL-3 laboratory, 3 mL of TA was dissociated using 50 µg/mL collagenase type 4 (Worthington), and 0.56 ku/mL of Dnase I (Worthington). The single-cells were collected by centrifugation and counted, and the CD45-positive cells were enriched using MojoSort Human CD45 beads (Biolgenend) and counted again before library preparation. For the whole-blood (WB) samples, the peripheral blood was collected into EDTA tubes (BD, 366643). 500 μl of peripheral blood was treated with RBC lysis buffer (Roche, 11-814-389-001) according to the manufacturer’s instructions and the single cells were collected and counted.
For both TA and WB samples, the Chromium Controller was loaded with 15,000 cells per sample following the manufacturer’s instructions (10X Genomics). Some samples were pooled together (at 15,000 cells per sample) before GEM partitioning. A Chromium Single Cell 5′ Reagent Kit v2 (10X Genomics) was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (following the detailed protocol provided by 10X Genomics). Libraries were sequenced on an Illumina NovaSeq6000.

tag: disease

value: whole-blood

value: Dex


title: RNAseq_neuron_wt_rep2

value: Cultured neurons (2 weeks in vitro) from E18.5 mouse embryo cortex


title: whole-blood, Dex, patient 415, scRNAseq


title: W82 H3K4me3 CUT&Tag rep1

city: Shanghai

institute: Fudan University

value: somatic cells


title: W82 H3K36me3 CUT&Tag rep2


title: AP2XII_9_CUT&Tag_2

value: co-culture with 500 uM IAA for 24 h


title: whole-blood, Dex, patient 414, scRNAseq


title: AP2XII_9_CUT&Tag_1


title: W82 H3K36me3 CUT&Tag rep1


title: PBMC, NoDex, patient 23, bulkRNAseq


title: RNAseq_brain_heter_rep4

value: Ctcf heterozygous mutated


title: W82 H3K27me3 CUT&Tag rep2


title: whole-blood, Dex, patient 412, scRNAseq


title: RNAseq_brain_heter_rep3


title: RNAseq_brain_heter_rep1


title: Liver, S9.6, IP, rep 2

city: Stanford

first: Mark

last: Kay

state: California

address: 269 Campus Drive CCSR Building, Room 2110

department: Pediatrics and Genetics

institute: Stanford University School of Medicine

data_processing:
*library strategy: DRIP-seq
Base calling CASAVA v1.8.2
Sequencing adapters were trimmed using cutadapt and then reads were aligned to genome build mm10 with bowtie2.
Reads were seperated into strands with unix processing tools.
Reads processed into bedpe format using bedtools
Reads sorted and duplicate reads were removed using unix text processing tools
Assembly: mm10
Supplementary files format and content: Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC
Supplementary files format and content: Deduplicated bam files from biological replicates were merged using samtools and then peaks were called between these merged input and IP files using MACS2 with default broad peak settings. Peak strand annotations were assigned by intersecting peaks with Gencode v25 mm10 genes extended up- and downstream by 3 kb using bedtools slop.

source_name: Liver

growth_protocol: HEPA1-6 cells were grown in DMEM media supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 IU/ml penicillin/streptomycin and in a humidified incubator at 37°C with 5% CO2. C57/Bl6 mice (JAX, 000664) were kept in the animal facility with a normal night/day cycle and on autoclaved chow ad libitum

extract_protocol:
genomic extraction was performed following step by step: High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing, Sanz and Chedin, Nature protocol, 2018
Prior to library preparation DNA was sonicated in Covaris microtubes (Fisher, 520045) to a peak fragment size of 300 bp, performed on a Covaris machine S220 using the following parameters: Intensity: 4, C/B: 200. DF: 10%, Time: 30 seconds. NEBNext® End Repair Module (NEB, E6050S) was used to repair the sonicated DNA and successively 3’ A-tails were added by Klenow Fragment (3'→5' exo-) (NEB, M0212S) and dATPs (NEB, N0440S). Next, adapters were ligated to the repaired DNA using the 1S Plus Set A Indexing Kit (Swift Biosciences), and DNA was then amplified by PCR (PE PCR Primer 1.0: 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’; PCR Primer 2.0: 5’ CAAGCAGAAGACGGCATACGA 3). For input libraries, 4 PCR cycles were used, while for IP libraries, 10 PCR cycles were needed. Following PCR amplification, DNA fragments between 200 and 600 bp were size selected using AMPure XP beads (Beckman Coulter, A63880). Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA) then pooled in equimolar ratios and sequenced on a HiSeq 4000 (Illumina, San Diego, CA, USA) at the Stanford Genome Sequencing Service Center, using 2x75bp sequencing

value: Liver

value: Hepatocyte

value: WT


title: LOiMAC,scRNAseq

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

country: South Korea

institute: Korea national institute of health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/5.0/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver organoid co-cultured with macrophage

extract_protocol:
The matrigel was gently removed by pipetting and spinning down liver organoids, and the organoids were then washed with co-culture media. Organoids were chopped into pieces and collected. Organoid fragments were repeatedly incubated and pipetted following TrypLE addition, and washed with co-culture media to make single cells. Following LUNA-fl cell counting, libraries for scRNA-seq were created in a 10x Chromium platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: LO,scRNAseq

description: 10x Genomics

source_name: liver organoid

value: liver organoid


title: whole-blood, Dex, patient 405, scRNAseq


title: W82 H3K27me3 CUT&Tag rep1

address: 2005 Songhu Rd

value: 17-day-old leaf

value: Williams 82


title: RNAseq_brain_heter_rep2

source_name: brain tissue from E18.5 mouse embryo

value: brain tissue from E18.5 mouse embryo


title: Liver, input rep 2


title: tracheal aspirate, NoDex, patient 89, scRNAseq

source_name: tracheal aspirate

value: tracheal aspirate

value: NoDex


title: RNAseq_brain_homo_rep1

value: Ctcf homozygous mutated


title: Liver, S9.6, IP,RNAseH1 rep 2


title: iMAC,scRNAseq

description: 10x Genomics

source_name: macrophage

value: macrophage


title: RNAseq_brain_wt_rep3

value: wild type


title: Liver, S9.6, IP,RNAseH1 rep 1


title: RNAseq_brain_homo_rep2


title: whole-blood, Dex, patient 402, scRNAseq

value: whole-blood

value: Dex


title: whole-blood, Dex, patient 403, scRNAseq


title: Ku80_CUT&Tag_1

value: tachyzoites

value: RH

value: co-culture with DMSO vehicle for 24 h


title: RNAseq_brain_wt_rep4


title: Liver, input rep 1

value: Liver


title: ND_hypoxia_input_rep2

city: Syracuse

first: Norifumi

last: Urao

state: New York

address: 750 E. Adams St.

department: Pharmacology

institute: SUNY Upstate Medical University

data_processing:
The fastq files were processed using PartekFlow  (Partek Inc., St. Louis, MO, USA).
The raw reads were aligned to mm10 with Bowtie2 and peaks were called by MACS2 with the significance cut-off q-value <=0.05.
Called peaks were quantified to regions and the normalization was performed with transcripts per million (TPM). The normalized peaks were then subjected to statistical analysis using Partek gene-specific analysis (GSA). Differential H3K4me3 peaks were identified with thresholds (p<0.05, least square mean > 20).
narrowpeak files were generated using MACS2 with default setting. Bigwig files were generated using bamCoverage on Galaxy.
Assembly: mm10
Supplementary files format and content: narrowpeak (except for Input sample)

source_name: Bone marrow derived macrophages

growth_protocol: BMDMs were derived from whole bone marrow cells and were cultured in DMEM with 10% FBS, pen/strep and 20ng/ml of M-CSF at 37C at 5% CO2. Media was changed to Macrophage-SFM with 20ng/ml of M-CSF at day4.

extract_protocol:
Cells were fixed with 0.4% paraformaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a M220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs. 2 ng of DNA was used as starting material for input and ip samples. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were cultured in 1% O2 hypoxia chamber for 1 hour at day7.

value: Bone marrow derived macrophages

value: Macrophages

value: Normal diet_hypoxia

tag: chip-ab


title: RNAseq_brain_wt_rep1


title: Liver, S9.6, IP, rep 1

value: Hepatocyte

value: WT

tag: treatment


title: tracheal aspirate, NoDex, patient 72, scRNAseq

tag: tissue


title: ND_hypoxia_input_rep3